I've tried to change '/' before RewriteBase to '/mysite', '/mysite/', '/mysite/shop', '/mysite/shop/', '/www/mysite' etc., non of my guesses worked.
Here is my .htaccess.
<IfModule mod_rewrite.c>
RewriteEngine On
##
# If you are getting 404 errors on subpages, you may have to uncomment the RewriteBase entry
# You should change the '/' to your appropriate subfolder. For example if you have
# your Grav install at the root of your site '/' should work, else it might be something
# along the lines of: RewriteBase /<your_sub_folder>
##
RewriteBase /mysite
# Access site
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php [L]
# Block various user files from being accessed directly
RewriteRule ^user/accounts/(.*)$ error [R=301,L]
RewriteRule ^user/config/(.*)$ error [R=301,L]
RewriteRule ^user/(.*)\.(txt|md|html|php|yaml|json|twig|sh|bat)$ error [R=301,L]
# Block cache/
RewriteRule ^cache/(.*) error [R=301,L]
# Block bin/
RewriteRule ^bin/(.*)$ error [R=301,L]
# Block system/
RewriteRule ^system/(.*)$ error [R=301,L]
# Block vendor/
RewriteRule ^vendor/(.*)$ error [R=301,L]
</IfModule>
# Prevent file browsing
Options -Indexes
I am not sure if I understand about setup info.